add cli

1/ exposes filter on target knockdown as something that can be run as:

uvx -q --from git+https://github.com/ArcInstitute/cell-load.git@cli_run_uv filter_on_target_knockdown --help

reverted breaking change for csr for colab notebook

Merge pull request #49 from dukesun99/patch-1

Fix CSR data types in _perturbation.py

properly cast all yielded tensors to torch.float32

0.7.5

merge main

support arbitrary globs in toml

users can now specify arbitrary glob and brace expressions in the dataset specifications, e.g.:

Dataset paths - maps dataset names to their directories

[datasets]
replogle = "/data/replogle/{jurkat,k562}.h5"

would only train on the jurkat and k562 files

remove X_hvg dependence

Merge pull request #47 from ArcInstitute/remove_hvg_dependence

fixes bug that requires X_hvg even when modeling with .X

fix pypi

this fixes breakages caused due to zclip and wandb

0.7.1

What's Changed

• Cleaned code for perturbation dataloaders by @abhinadduri in #2
• 4 setup ci for testing and installing by @noamteyssier in #5
• 6 rename to vc load by @noamteyssier in #7
• Lightning datamodule setup requires stage by @sravya8 in #10
• added var names for test datasets to have access to .var.index by @abhinadduri in #15
• 12 convert package name to cell load by @noamteyssier in #16
• changed data loader key names by @abhinadduri in #20
• switched to a toml based way to specify perturbations by @abhinadduri in #21
• Kd efficiency by @yhr91 in #24
• additional cell KD filter by @yhr91 in #25
• Fix var names by @abhinadduri in #26
• bugfix by @abhinadduri in #27
• remove bug for double log by @abhinadduri in #29
• updating the way gene names are fetched for group objects by @rohankshah04 in #31
• 30 fix implicit circular imports and use explicit typing by @noamteyssier in #32
• 33 replace lambda function with a partial by @noamteyssier in #34
• 36 fix remaining check errors and introduce ruff check into ci by @noamteyssier in #37
• minor fix to make cell-load compatible to baselines by @Naghipourfar in #40
• ci: added release ci by @noamteyssier in #42
• chore: move examples to subdir by @noamteyssier in #44

New Contributors

• @abhinadduri made their first contribution in #2
• @noamteyssier made their first contribution in #5
• @sravya8 made their first contribution in #10
• @yhr91 made their first contribution in #24
• @rohankshah04 made their first contribution in #31
• @Naghipourfar made their first contribution in #40

Full Changelog: https://github.com/ArcInstitute/cell-load/commits/0.7.1